Number of runs: 1
Number of samples (input count >0): 341
Number of controls: 0 3 samples with <1M reads after quality
filtering in taxonomy module excluded (M001BS3, M077BS3, and
M104BS3)
India Malawi
BS3 283 58
country n min med max
1 India 283.0 999999.1 1000000.0 1000000.9
2 Malawi 58.0 999999.2 1000000.0 1000000.6
No additional filtering required given that normalised pathway data (copies per million) serves as input.
Number of functional pathways included: 2387
Number of samples included: 341
R version 4.2.1 (2022-06-23)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur ... 10.16
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib
locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] Maaslin2_1.10.0 FSA_0.9.3 ALDEx2_1.28.1
[4] zCompositions_1.4.0-1 truncnorm_1.0-8 NADA_1.6-1.1
[7] survival_3.4-0 MASS_7.3-58.1 sjstats_0.18.1
[10] ggExtra_0.10.0 formattable_0.2.1 inlmisc_0.5.5
[13] wesanderson_0.3.6 phangorn_2.10.0 ape_5.6-2
[16] DECIPHER_2.24.0 RSQLite_2.2.18 Biostrings_2.64.1
[19] GenomeInfoDb_1.32.4 XVector_0.36.0 IRanges_2.30.1
[22] S4Vectors_0.34.0 BiocGenerics_0.42.0 cowplot_1.1.1
[25] scales_1.2.1 RVAideMemoire_0.9-81-2 DescTools_0.99.47
[28] ggsignif_0.6.4 binom_1.1-1.1 shiny_1.7.3
[31] randomcoloR_1.1.0.1 crossval_1.0.4 labdsv_2.0-1
[34] mgcv_1.8-41 nlme_3.1-160 ggpubr_0.4.0
[37] data.table_1.14.4 corrplot_0.92 vegan_2.6-4
[40] lattice_0.20-45 permute_0.9-7 randomForest_4.7-1.1
[43] matrixStats_0.62.0 lme4_1.1-30 Matrix_1.5-1
[46] reshape2_1.4.4 pheatmap_1.0.12 DT_0.26
[49] plotly_4.10.0 cluster_2.1.4 tidyr_1.2.1
[52] dplyr_1.0.10 magrittr_2.0.3 plyr_1.8.7
[55] kableExtra_1.3.4 gridExtra_2.3 RColorBrewer_1.1-3
[58] knitr_1.40 ggplot2_3.3.6 phyloseq_1.40.0
loaded via a namespace (and not attached):
[1] estimability_1.4.1 coda_0.19-4
[3] bit64_4.0.5 DelayedArray_0.22.0
[5] RCurl_1.98-1.9 generics_0.1.3
[7] terra_1.6-17 proxy_0.4-27
[9] bit_4.0.4 webshot_0.5.4
[11] xml2_1.3.3 httpuv_1.6.6
[13] SummarizedExperiment_1.26.1 assertthat_0.2.1
[15] xfun_0.34 jquerylib_0.1.4
[17] evaluate_0.17 promises_1.2.0.1
[19] DEoptimR_1.0-11 fansi_1.0.3
[21] readxl_1.4.1 igraph_1.3.5
[23] DBI_1.1.3 htmlwidgets_1.5.4
[25] purrr_0.3.5 ellipsis_0.3.2
[27] backports_1.4.1 V8_4.2.1
[29] insight_0.18.6 MatrixGenerics_1.8.1
[31] vctrs_0.5.0 Biobase_2.56.0
[33] sjlabelled_1.2.0 abind_1.4-5
[35] cachem_1.0.6 withr_2.5.0
[37] robustbase_0.95-0 rgdal_1.5-32
[39] emmeans_1.8.2 getopt_1.20.3
[41] svglite_2.1.0 lazyeval_0.2.2
[43] crayon_1.5.2 flexdashboard_0.6.0
[45] pkgconfig_2.0.3 rlang_1.0.6
[47] lifecycle_1.0.3 miniUI_0.1.1.1
[49] modelr_0.1.9 cellranger_1.1.0
[51] datawizard_0.6.3 raster_3.6-3
[53] carData_3.0-5 lpsymphony_1.24.0
[55] Rhdf5lib_1.18.2 boot_1.3-28
[57] viridisLite_0.4.1 parameters_0.19.0
[59] rootSolve_1.8.2.3 bitops_1.0-7
[61] rhdf5filters_1.8.0 blob_1.2.3
[63] stringr_1.4.1 rstatix_0.7.0
[65] memoise_2.0.1 zlibbioc_1.42.0
[67] compiler_4.2.1 cli_3.4.1
[69] ade4_1.7-19 tidyselect_1.2.0
[71] stringi_1.7.8 highr_0.9
[73] yaml_2.3.6 grid_4.2.1
[75] sass_0.4.2 fastmatch_1.1-3
[77] tools_4.2.1 lmom_2.9
[79] rstudioapi_0.14 foreach_1.5.2
[81] optparse_1.7.3 gld_2.6.6
[83] farver_2.1.1 Rtsne_0.16
[85] RcppZiggurat_0.1.6 digest_0.6.30
[87] quadprog_1.5-8 Rcpp_1.0.9
[89] GenomicRanges_1.48.0 car_3.1-1
[91] broom_1.0.1 performance_0.10.0
[93] later_1.3.0 httr_1.4.4
[95] effectsize_0.8.1 colorspace_2.0-3
[97] rvest_1.0.3 splines_4.2.1
[99] expm_0.999-6 sp_1.5-0
[101] multtest_2.52.0 Exact_3.2
[103] systemfonts_1.0.4 xtable_1.8-4
[105] jsonlite_1.8.3 nloptr_2.0.3
[107] Rfast_2.0.6 R6_2.5.1
[109] pillar_1.8.1 htmltools_0.5.3
[111] mime_0.12 glue_1.6.2
[113] fastmap_1.1.0 minqa_1.2.5
[115] BiocParallel_1.30.4 class_7.3-20
[117] codetools_0.2-18 pcaPP_2.0-3
[119] mvtnorm_1.1-3 utf8_1.2.2
[121] bslib_0.4.0 tibble_3.1.8
[123] curl_4.3.3 biglm_0.9-2.1
[125] rmarkdown_2.17 biomformat_1.24.0
[127] munsell_0.5.0 e1071_1.7-12
[129] rhdf5_2.40.0 GenomeInfoDbData_1.2.8
[131] iterators_1.0.14 sjmisc_2.8.9
[133] gtable_0.3.1 bayestestR_0.13.0
.